Well in the case of the Cabal bunkers, since the Cabal are a huge empire spanning I don't know how many star systems, I'm pretty sure they can make bunkers impervious to nuclear damage. Maybe not impervious to fallout, but they could survive the blast and live self-sustained for a while. And the Hive have also conquered thousands of planets, and their caves on the Moon span for miles, far out of reach of nuclear weaponry (except maybe a [url=http://halo.wikia.com/wiki/NOVA_Bomb]Nova bomb[/url], but that's a different universe).